MarioniLab scran issues

MarioniLab / scran

Clone of the Bioconductor repository for the scran package.

https://bioconductor.org/packages/devel/bioc/html/scran.html

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issues

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Feature Request: pseudoBulkDGE for Non-Integer Batch-corrected Data

#120 DarioS opened 1 week ago
1
pseudoBulkDGE - logFC means upregulated in which condition?

#119 jcasadogp opened 2 months ago
1
Cyclone Computational Efficiency

#118 DarioS closed 3 months ago
3
Error with cyclone

#117 SarahE97 opened 3 months ago
1
rank.logFC.detected Produces Dubious Rankings

#116 DarioS opened 5 months ago
4
Integer Overflow

#115 DarioS closed 5 months ago
2
`scran::findMarkers` always return all available markers as differential, albeit with different p-values

#114 denvercal1234GitHub closed 10 months ago
4
sizeFactors for mixed patient samples

#113 flde closed 8 months ago
2
Marker detection in multimodal data

#112 PeteHaitch opened 11 months ago
1
`scoreMarkers()`: Parallelisation changes `rank.*` statistics

#111 PeteHaitch closed 11 months ago
2
DEG results only contain downregulated gene

#110 littleju777 closed 1 year ago
2
fix error unused argument objective_function when pass both block and graph.fun

#109 Yunuuuu opened 1 year ago
0
Error in FUN(x, table, nomatch = nomatch, incomparables = incomparables) : 'match' requires vector arguments

#108 galaxyeee opened 1 year ago
3
add weights in pseudbulkDGE for edgeR analysis

#107 koenvandenberge opened 1 year ago
4
cant load scran

#106 christoforos-dimitropoulos closed 1 year ago
6
Implement the https://satijalab.org/seurat/reference/findsubcluster

#105 Yunuuuu closed 1 year ago
10
Old versions disappeared from bioconductor?

#104 scottgigante-immunai closed 1 year ago
3
Error normalizing Anndata

#103 Mari123i opened 1 year ago
0
Depreciated scran functions and commands. Any updated tutorial?

#102 levinhein opened 1 year ago
0
scran normalize

#101 jayypaul opened 2 years ago
1
Different list for findmarker function

#100 angkoomin opened 2 years ago
1
Receiving 'ref.clust' not in 'clusters' for cluster label that is part of predefined clusters

#99 xlancelottx closed 2 years ago
5
Cyclone not finishing when using BPPARAM=MulticoreParam(workers = n))

#98 Hrovatin opened 2 years ago
0
BiocParallel errror (invalid length of row names) in combineMarkers() with full.stats = TRUE

#97 CyrilLagger closed 2 years ago
2
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"dgRMatrix", "character"’

#96 houruiyan opened 2 years ago
1
escape % in Roxygen doc

#95 bug1303 closed 2 years ago
1
Add lfc= option back to scoreMarkers

#94 LTLA closed 3 years ago
0
error using scaledColRanks

#93 doliv071 closed 3 years ago
3
A simpler, more streamlined function to compute marker scores.

#92 LTLA closed 3 years ago
0
Installation is failing

#91 prvst closed 3 years ago
6
`pseudoBulkDGE()` intermediates dropped if `row.data` supplied

#90 PeteHaitch closed 3 years ago
1
findmarkers summary.logFC values

#89 cstrlln closed 4 months ago
1
Fall back to combining pure one-sided tests for direction=any.

#88 LTLA closed 3 years ago
0
Installation of package ‘scran’ had non-zero exit status

#87 awurmser opened 3 years ago
2
findMarkers produces unexpectedly different results with passing different values to direction

#86 wir963 closed 3 years ago
11
inter-cluster rescaling factors are not strictly positive

#85 Hrovatin closed 3 years ago
2
Add a fixedPCA function to avoid relying on scater::runPCA

#84 LTLA closed 3 years ago
1
getTopHVGs should just call modelGeneVar if applied on an SCE

#83 LTLA closed 3 years ago
0
Can I use BuildSNNGraph on scWGBS data?

#82 xiaonian92 opened 3 years ago
2
"assay.type" in the modelGeneVarByPoisson man page

#81 ycl6 closed 3 years ago
1
psuedoBulkDGE

#80 elachtarajax opened 3 years ago
5
Streamlined the correlation computation machinery.

#79 LTLA closed 3 years ago
0
decideTestsPerLable() ignores value of pval.field

#78 PeteHaitch closed 3 years ago
2
DESCRIPTION: add links to GitHub

#77 mr-c opened 3 years ago
2
Use bluster::clusterRows by default in getClusteredPCs

#76 LTLA closed 3 years ago
0
Implement bootstrapCluster for clusters generated in Seurat

#75 lucygarner opened 3 years ago
6
Error in denoisePCA : NA indices are not supported for sparse matrix

#74 ljouneau closed 3 years ago
5
Pseudobulk DGE

#73 jennapappalardo closed 3 years ago
4
Began the transition towards beachmat version 3.

#72 LTLA closed 3 years ago
0
Scran normalisation for Single cell allelic data

#71 DeepshikhaChandel closed 3 years ago
4